1.0 Running Clustergrammer2

This notebook demonstrates how Clustergrammer2 can be used to visualize two simple datasets.

import numpy as np
import pandas as pd
from clustergrammer2 import net
import warnings
warnings.filterwarnings('ignore')

>> clustergrammer2 backend version 0.5.2

Load Dataset

Try replacing this dataset with your own, by uploading data through Jupyter Lab.

net.load_file('../data/rc_two_cats.txt')
df = net.export_df()
df.shape

(38, 29)

View Toy Dataset

import ipywidgets
ipywidgets.__version__

'7.5.1'

import nbconvert

nbconvert.__version__

'5.3.2.dev0'

net.load_df(df)
net.widget()

Generate Random Matrix

# generate random matrix
num_rows = 1000
num_cols = 1000
np.random.seed(seed=100)
mat = np.random.rand(num_rows, num_cols)

# make row and col labels
rows = range(num_rows)
cols = range(num_cols)
rows = [str(i) for i in rows]
cols = [str(i) for i in cols]

# make dataframe 
df = pd.DataFrame(data=mat, columns=cols, index=rows)
df.shape

(1000, 1000)

net.load_df(df)
net.widget()

# net.load_df(df)
# net.widget()

TMP!!! no widgets